[gmx-users] Literature for DNA Binding Protein Simulations

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 23 00:39:36 CET 2010

Arden Perkins wrote:
> Dear GROMACS users, I am interested in running a simulation of a 
> DNA-binding peptide and a short stretch of DNA for an undergraduate 
> research project. The pdb file we will be using is a modified version of 
> the Hickman et. al (2004) Rep structure 
> http://www.pdb.org/pdb/explore/explore.do?structureId=1RZ9 . The file 
> consists of five Rep peptides and one stretch of DNA (approx. 6 helical 
> turns). We will only be simulating one peptide however, at 197 aa. We 
> would like to subject the peptide to different variables in a 
> water-solvated box and then observe its interaction with the segment of 
> DNA to which it binds (such as temperature, ion molarities, etc).
> What literature would you recommend I review in order to have a good 
> understanding of the parameters involved in such a simulation? I 
> have run simulations of this peptide in solvated systems before, but I 
> have never attempted one with more than one peptide or a peptide with DNA.

A Google Scholar search for "protein-DNA molecular dynamics" yields several 
thousand results.  Surely, somewhere in there you'll find some useful information.

The run parameters will be largely dictated by the force field you choose for 
such a task.  I frequently see AMBER force fields used for such applications, 
but that choice should be motivated by what your reading tells you.

As for building the system, it should not be that different from what you're 
used to.  There are no tutorials specifically for this task (that I am aware 
of), nor will the literature tell you how to set these systems up. 
Understanding Gromacs topologies is pretty much the only pre-requisite.  I would 
suggest you give it a shot and if you have specific questions, post them; it 
will be much easier to help diagnose specific issues.  It's very hard to address 
a question like "how should I do this project?"


> Any suggestions would be very appreciated.
> Arden Perkins


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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